BtaEX0017355 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000003304 | HOXC4
Description
Bos taurus homeobox C4 (HOXC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001102373]
Coordinates
chr5:26136686-26149357:-
Coord C1 exon
chr5:26139417-26149357
Coord A exon
chr5:26138335-26138779
Coord C2 exon
chr5:26136686-26137850
Length
445 bp
Sequences
Splice sites
3' ss Seq
AAAATTATTTTCCACTCCAGAAA
3' ss Score
6.59
5' ss Seq
CGGGTAGGC
5' ss Score
7.5
Exon sequences
Seq C1 exon
TGGGGATGCGTGTTTACATGTAAACACATGTGTTACATGGATACAATCCCTGGCCGGAAGCAGGCTCTACTAACGCAGGCCTTCCTCCTAGCTAGGTCTGCCCTCTGTGGGGATGGAGAAGGAAGAGCTCCCAGGGCCTTGGCTGGGCACCATCCCAGGGGACTGGCCCCTGGCAGAGTGCTCTCCTCCTTGCCCCAGGTCCTCGGGAACCGGCCTTGGAGGTAGTTGTCAGAAAGCGGCAGGCCAGGCAGAATGGAGAGCAGAAACAACTGCCAGCGGAAGAGATCCTCTGCTCCAGGCTGGGCAGGGAGGGTCAGTGGGCACTTGGGGAGGGCAAGGCTTCTGAACTATGCTTTTGCCAACCACTTCCTGTCTCTCTTCAGCGGGGGCTCAACCCCCAGACCTCCAGAAATGACGTCAGAATCATTTGCATCCCGCTGCCTCTACCTGCCTGGTCCAGCTGGGACCCTGCCTCGCCGGCCCCCTGGCCAGAGGGTTGG
Seq A exon
AAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCATGCGAAGAATATTCGCAAAATAGCTACATCCCTGAACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATCACCACCAGGAGCTGTACCCACCACCGCCTCCGCGCCCTAGCTACCCTGAGCGCCAGTATAGCTGCACCAGTCTCCAGGGGCCGGGCAATTCGCGAGGCCACGGGCCGGCCCAGGCGGGCCACCACCACCCCGAGAAATCACAGCCGCTCTGCGAGCCGGCGCCTCTCTCAGGCGCCTCCGCCTCCCCGTCCCCAGCCCCGCCAGCCTGCAGCCAGCCAGCCCCTGACCATCCCTCCAGCGCCGCCAGCAAGCAACCCATAGTCTACCCATGGATGAAAAAAATCCACGTTAGCACGG
Seq C2 exon
TGAACCCCAATTATAACGGAGGGGAACCCAAGCGCTCGAGGACAGCCTACACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACAATCGCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCTCTGAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGCATGAAATGGAAGAAGGACCACCGACTTCCCAACACCAAAGTCAGGTCAGCGCCCCCGGCCGGCGCTGCGCCCAGCACCCTCTCCGCAGCCACCCCGGGCACTTCTGAAGACCACTCCCAGAGCGCCACGCCGCCGGAGCAGCAACGGGCAGAGGACATTACCAGGTTATAAAACATAACTCACACCCTGCCCCTATCCCAGGCCCCCCATCCTCCCCTCACACACAAATTGACTCTTATTTATAGAATTTAATATATATATATATTTTGGTTCTTTTCTCTCTTCCTCCCACCTTCCCCCTTGTCAGTTCCAAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003304_MULTIEX1-1/2=C1-C2
Average complexity
C2*
Mappability confidence:
100%=100=100%
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=NA A=0.796 C2=0.669
Domain overlap (PFAM):
C1:
NA
A:
NO
C2:
PF0004624=Homeobox=WD(100=47.9)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAAGAGATCCTCTGCTCCA
R:
TCGATCCTTCTCCTTCGGGTC
Band lengths:
348-793
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development